Evolution of Human WSN/33 in Swine in Korea in 2005
Recombinomics Commentary
April 28, 2005
Analysis of the 2005 WSN/33 H1 sequences in fatal infections of Korean pigs reveals many new polymorphisms which appear to have been acquired in the past several months. Approximately 600 bp of H1 have been determined for each of two 2 H1N1 isolates and 7 lung extracts. In the region sequenced, there were six polymorphisms unique to WSN/33, and all six are present in the 2005 isolates, as is a 3 nucleotide deletion. The two H1N1 2004 swine isolates deposited at GenBank had an additional polymorphism not found in WSN/33, and that polymorphism is also present in all nine 2005 sequences. The two 2005 isolates have three additional polymorphisms. Two are unique to the 2005 isolates and a third was found in one of the two 2004 isolates.
The 7 PCR sequences reveal additional polymorphisms. One sequence is unique, with 9 unique polymorphisms. The other 6 sequences share a number of polymorphisms and form small clades. Two of the sequences match each other, but additional polymorphisms found in three or four of the six sequences create the clades. In addition, there are a number of unique polymorphisms found in the PCR sequences.
Thus, it seems quite clear that while the WHO was trying to prove that the WSN/33 sequences were lab artifacts, the viruses containing the WSN/33 sequences were infecting and killing pigs in South Korea. South Korea provides a rich genetic environment for evolutionary change. Last year H9N2, H3N2, and H6N1 isolates were found in live markets in South Korea. In addition, there was an H5N1 outbreak last season and H5N2 was detected this season. Recently WHO announced that although they had failed to prove that WSN/33 did not exist in Korean swine, they were able to isolate H1N2 in swine, which was similar to a 2002 Korean isolate as well as isolates found in the United States.
WHO's effort in the past 6 months deserves some attention. In December they concluded that WSN/33 did not exist in swine in Korea and the sequences deposited at GenBank on Oct 24, 2004 were lab errors. In fact some journalists were told that the sequences may have been accidentally uploaded or e-mailed to GenBank, suggesting the researcher depositing the sequence didn't realize the sequences contained genes of WSN/33. Since the 30 of the 48 genes were WSN/33, submitting that many files in error would be difficult, especially since the sequences were not exact matches of WSN/33 and were not exact matches of each other. Moreover, the WHO consultants knew that the sequences were the subject of a manuscript that had been submitted for peer review, so there was no chance that the researcher did not know that the submitted sequences contained 30 WSN/33 genes. However, the recent WHO announcement still refers to the sequences as being "uploaded" to GenBank, trying to keep the memory of the virtual WSN/33 sequences alive.
Unfortunately, the real genes were alive and well in Korean swine. They were spreading and evolving and creating associations with dead swine and aborted swine fetuses. This evolution continued as WHO brought in more consultants to show that the WSN/33 sequences did not exist. Some may have viewed the task as an academic exercise, because they were unaware of the fact that two of the six sequences were H1N1, which would be capable of efficient human-to-human transmission. They were under the impression that all of the isolates were avian H9N2, with a few human genes mixed in by error.
Since WHO did not prove the two H1N1 isolates from 2004 were lab errors, it is unlikely that they will be able to disprove the existence of the 9 new sequences, since they have even more diversity. Moreover 7 not only did not require cell lines for isolation, but they were generated by PCR reactions using lung extracts from dead pigs.
WHO did prove that their experts and animal quarantine in Korea could not detect the WSN/33 sequences, and like H5N1 bird flu in Vietnam, the monitoring of pandemic flu in Korea is well beyond scandalous.